Browsing by Subject "Energy landscape"
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Item Direct measurement of the energy landscape of ligand-receptor interactions(2010-08) Schwemmer, Frank Heinz, 1986-; Florin, Ernst-Ludwig; Shubeita, George T.In this thesis, a novel single molecule technique will be presented that will, for the first time, give direct access to the interaction energy landscapes of small molecules. The technique relies on the interpretation of thermal position fluctuations of a colloidal probe particle tethered to the molecular complex of interest and a geometrical amplification effect that converts Ångstrom scale fluctuations of the ligand in the binding pocket of the receptor to tens of nanometer fluctuation of the bead. The position of the bead is measured with 0.5 MHz bandwidth and 2 nm spatial resolution. The surface characteristic of the substrate was found to be critical for this new technique and various surface effects were observed. Methods were developed to block nonspecific interaction between the surfaces. The mobility of specifically bound particles was found to depend strongly on the density of specific bonds and the length of the molecular complex; low concentration and short linker lead to slow ligand-receptor mediated surface diffusion, high concentration and/or long linkers to an immobilization of the particle. Transient bond formation was observed for the intermediate range. Details of the interaction energy landscape were not resolved. However, a systematic change in the linker length from 22 Å to 29 Å led to a corresponding change in the lateral position fluctuations from 12.9 nm to 13.2 nm in excellent agreement with our theoretical calculations, confirming the geometrical amplification effect. Also, a new phenomenon of nanometer scale friction in the gap between the bead and the surface was discovered. In summary, the results underline that the novel technique might be able to measure details of the interaction energy landscape of a specific ligand-receptor bond and thus test theoretical predictions for its shape.Item Energy landscape and electric field mediated interfacial colloidal assembly(Texas A&M University, 2007-09-17) Bahukudumbi, PradipkumarChemically and physically patterned surfaces can be used as templates to guide nano- and micro- scale particle assembly, but the design is often limited by an inability to sufficiently characterize how pattern features influence local particle-surface interactions on the order of thermal energy, kT. The research outlined in this dissertation describes comprehensive optical microscopy (i.e. evanescent wave, video) measurements and analyses of many-body and multi-dimensional interactions, dynamics and structure in inhomogeneous colloidal fluid systems. In particular, I demonstrate how non-intrusive observation of an ensemble of particles diffusing past each other and over a physically patterned surface topography can be used to obtain sensitive images of energy landscape features. I also link diffusing colloidal probe dynamics to energy landscape features, which is important for understanding the temporal imaging process and self-assembly kinetics. A complementary effort in this dissertation investigated the use of external AC electric fields to reversibly tune colloidal interactions to produce metastable ordered configurations. In addition, the electrical impedance spectra associated with colloidal assemblies formed between interfacial microelectrode gaps was measured and consistently modelled using representative equivalent circuits. Significant results from this dissertation include the synergistic use of the very same colloids as both imaging probes and building blocks in feedback controlled selfassembly on patterns. Cycling the AC field frequencies was found to be an effective way to anneal equilibrium colloidal configurations. Quantitative predictions of dominant transport mechanisms as a function of AC electric field amplitude and frequency were able to consistently explain the steady-state colloidal microstructures formed within electrode gaps observed using video microscopy. A functional electrical switch using gold nanoparticles was realized by reversibly forming and breaking colloidal wires between electrode gaps. Extension of the concepts developed in this dissertation suggest a general strategy to engineer the assembly of colloidal particles into ordered materials and controllable devices that provide the basis for numerous emerging technologies (e.g. photonic crystals, nanowires, reconfigurable antennas, biomimetic materials).Item Exploring energy landscapes of solid-state materials : from individual atoms to collective motions(2014-05) Xiao, Penghao; Henkelman, GraemeChemical reactions can be understood as transitions from basin to basin on a high dimensional potential energy landscape. Varying temperature only changes the average kinetic energy of the system. While applying voltages or external pressures directly tilts the landscape and drives the reactions in desired directions. In solids at relatively low temperature, where the entropy term is approximately invariant, the reaction spontaneity is determined by the energy difference between the reactant and product basins and the reaction rate can be calculated from the barriers in between. To achieve sufficient accuracy to explain experimental observations we are interested in, density functional theory (DFT) is usually employed to calculate energies. There are two types of reactions I have studied: the first type of reaction only involves a few number of individual atoms, corresponding to traveling in a small volume in the high dimensional configuration space; the other type involves a large amount of atoms moving in a concerted pattern, and the distance traveled in the configuration space is significantly longer. The scopes of these two in the energy landscapes are in different scales and thus proper metrics for distance measurements are required. In the first case, I have mainly studied Li/Na behaviors in the cathode materials of secondary batteries. Here resolving the energy landscape step by step with detailed information is possible and useful. By analyzing the energy landscapes with DFT plus the Hubbard U correction, I have explained several phenomena related to the degradation of lithium-rich layered oxides, rate performance of surface modified LiFePO₄, and capacity of vanadium-based fluorophosphates. Predictions on both thermodynamic and kinetic properties of materials are also made based on the calculation results and some are confirmed by experiments. In the second case, my focus is on solid-solid phase transitions. With a tremendous long reaction pathway, examining every possible atomic step is too expensive. By adopting periodic boundary conditions, a small supercell can represent the main feature of the energy landscape in a coarse grained way, where the connection between phases is easier to explore. After the big picture of a phase transition mechanism learned from this simplified model, details along the reaction pathway, like new phase nucleation and growth, could be resolved by using a larger supercell. In the above treatment, two types of variables, the cell vectors and atomic positions, span a generalized configuration space. Special consideration is required to balance these two to keep consistency under different supercells and avoid biases. A solid-state NEB (SSNEB) and a solid-state dimer (SSD) method are then developed to locate saddle points in the generalized configuration space. With the methodology well justified, we are able to efficiently find possible nucleation mechanisms, for examples the CdSe rock salt to wurtzite and Mo A15 to BCC phase transitions. SSNEB is also applied in studying phases transitions under pressures, including the graphite to diamond, and CaIrO₃ perovskite to post-perovskite transitions. Combined with the adaptive kinetic Monte Carlo (AKMC) algorithm, SSD shows the ability to find new polymorphs of CdSe and the connecting barriers between them.Item Ultra-precise manipulation and assembly of nanoparticles using three fundamental optical forces(2012-12) Demergis, Vassili; Florin, Ernst-Ludwig; Shubeita, George T; Fink, Manfred; Makarov, Dmitrii E; Korgel, Brian AThe invention of the laser in 1960 opened the door for a myriad of studies on the interactions between light and matter. Eventually it was shown that highly focused laser beams could be used to con fine and manipulate matter in a controlled way, and these instruments were known as optical traps. However, challenges remain as there is a delicate balance between object size, precision of control, laser power, and temperature that must be satisfied. In Part I of this dissertation, I describe the development of two optical trapping instruments which substantially extend the allowed parameter ranges. Both instruments utilize a standing wave optical field to generate strong optical gradient forces while minimizing the optical scattering forces, thus dramatically improving trapping efficiency. One instrument uses a cylinder lens to extend the trapping region into a line focus, rather than a point focus, thereby confining objects to 1D motion. By translation of the cylinder lens, lateral scattering forces can be generated to transport objects along the 1D trapping volume, and these scattering forces can be controlled independently of the optical gradient forces. The second instrument uses a collimated beam to generate wide, planar trapping regions which can con fine nanoparticles to 2D motion. In Part II, I use these instruments to provide the first quantitative measurements of the optical binding interaction between nanoparticles. I show that the optical binding force can be over 20 times stronger than the optical gradient force generated in typical optical traps, and I map out the 2D optical binding energy landscape between a pair of gold nanoparticles. I show how this ultra-strong optical binding leads to the self-assembly of multiple nanoparticles into larger contactless clusters of well de ned geometry. I nally show that these clusters have a geometry dependent coupling to the external optical field.